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  • Filtering and trimming data

    Is there a stand alone program (i.e. not incorporated into Velvet, Bowtie etc) that I can use to filter and trim Illumina fastq sequences

    thanks

  • #2
    fastx toolkit

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    • #3

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      • #4
        While not exactly standalone, there are a bunch filtering and QC options on the public Galaxy server. Go to usegalaxy.org and click on "NGS: QC and manipulation" in the left bar.

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        • #5
          R / Bioconductor has flexible tools in the ShortRead, Biostrings, and GenomicRanges packages. Some relevant functions include readFastq, writeFastq, SRFilter, trimLRPatterns, alphabet, alphabetByCycle, narrow, trimTails (in the `devel` branch), ...

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          • #6
            A new one: Btrim

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            • #7
              Originally posted by steven View Post
              A new one: Btrim
              It would be helpful if these kind of tools would be aware of paired-ends and keep the final output file(s) synced (in terms of of read/mate positions/existence in output).
              Just a thought :-)

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              • #8
                TRimming FASTQ file

                Dear,

                I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do i need to trim the line having qual score as well?

                With REgards
                Parveen Kumar

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                • #9
                  Originally posted by parveendabas View Post
                  Dear,

                  I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do i need to trim the line having qual score as well?

                  With REgards
                  Parveen Kumar
                  Yes, that would be correct. Trim the qual score too.

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                  • #10
                    You should be able to trim reads directly, at least I know you can with Bowtie. Lok at the available options for all these tools.

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                    • #11
                      thank you... cheers.

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